https://github.com/applicativesystem/rust-samtools-genomeview

rust-samtools-genomeview
https://github.com/applicativesystem/rust-samtools-genomeview

bioinformatics genome-alignments genome-analysis genome-bioinformatics genome-capture genome-sequencing

Last synced: 7 days ago
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rust-samtools-genomeview

• Host: GitHub
• URL: https://github.com/applicativesystem/rust-samtools-genomeview
• Owner: applicativesystem
• License: mit
• Created: 2024-12-04T21:34:31.000Z (18 days ago)
• Default Branch: main
• Last Pushed: 2024-12-13T21:03:27.000Z (9 days ago)
• Last Synced: 2024-12-13T22:18:15.493Z (9 days ago)
• Topics: bioinformatics, genome-alignments, genome-analysis, genome-bioinformatics, genome-capture, genome-sequencing
• Language: Rust
• Homepage:
• Size: 14.8 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# rust-samtools-genomeview

- rust samtools genome-view

- rust-samtools-genome-view: takes a genome alignment files, a reference fasta file, the upstream and the downstream regions and the path to the prank aligner and then aligns the extracted regions and also outputs a unaligned file.The aligned region will also be visualized into the terminal using the embedded approach. 

- This feature is not present in samtools and specific to rust-samtools and allows for the direct estimation of the reads to alignments approach for desining capture assay.

- targetd capture assay development for taking reads from HybSeq.

- general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.

![](https://github.com/applicativesystem/rust-samtools-genomeview/blob/main/rust-samtools-genomeview.png)

```

cargo build 

```

```

λ gauravsablok rust-samtools-genomeview → λ git main* → \

./target/debug/rust-samtools-genome-view -h

Usage: rust-samtools-genome-view      

Arguments:

        please provide the path to the alignment file

           please provide the id list for the specific region

            please provide the fasta file used for the reference alignment

         please provide the upstream add from the sam alignments to be extracted

       please provide the downstream add from the sam alignments to be extracted

    please provide the path to the prank aligner

Options:

  -h, --help     Print help

  -V, --version  Print version

```

- how to run the binary

```

./rust-samtools-genome-view ./sample-files/Col0_C1.100k_selected.sam ./sample-files/idlist.txt ./sample-files/sample-fasta.fasta 5 10 ./prank

```

- it will output following additional files

```

- selected-ids-downstream-aligned.fasta.best.fas - best alignment for the downstream region

- selected-ids-reads-aligned.fasta.best.fas - best alignment for the reads

- selected-ids-upstream-aligned.fasta.best.fas - best alignment for the upstream region.

- selected-ids-upstream-region-downstream-aliged.fasta.best.fas - best alignment for the upstream+region+downstream.

Gaurav Sablok